How to create ouput file using perl

Question

[vinij80]

I have two files.One file contains blast result of contigs and the next file contains the contigs that are used for blast.I want an output text file of sequences in a separate folder which gives no hits in blast result from original fasta file with all contigs. I have no idea about this.Can you please help me to create perl script for this problem.

[roy.granit]

Can you provide a short sample for each of the files?

[vinij80]

BLAST RESULT FILE

	BLASTN 2.2.31+
	Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb
	Miller (2000), "A greedy algorithm for aligning DNA sequences", J
	Comput Biol 2000; 7(1-2):203-14.
	Database: Arabidopsis_thaliana.mRNA.EST.fasta
	1,529,700 sequences; 400,627,814 total letters
	Query= Contig1
	Length=941
	Score E
	Sequences producing significant alignments: (Bits) Value
	gi|61656031|gb|DN604734.1|DN604734 EST JCAt1g22640 Arabidopsis ... 219 4e-055
	> gi|61656031|gb|DN604734.1|DN604734 EST JCAt1g22640 Arabidopsis
	Gateway cDNA Library Arabidopsis thaliana cDNA 3', mRNA sequence.
	Length=740
	Score = 219 bits (118), Expect = 4e-055
	Identities = 263/334 (79%), Gaps = 6/334 (2%)
	Strand=Plus/Minus
	Query 60 AAAGGAGCTTGGACTAAAGAAGAAGATGAACGACTTATTTCTTATAT--TAAAACTCACG 117
	||||||||||||||||||||||||||| | | ||| || ||| || ||| ||||
	Sbjct 734 AAAGGAGCTTGGACTAAAGAAGAAGATCAGCTTCTTGTTGATTACATCCGTAAA--CACG 677
	Query 118 GCGAAGGTTGCTGGAGATCCCTTCCTAAAGCTGCCGGACTTCTCCGATGCGGTAAAAGTT 177
	| |||||||||||| |||| || ||| || || ||| | | |||| ||||| ||||
	Sbjct 676 GTGAAGGTTGCTGGCGATCTCTCCCTCGCGCCGCTGGATTACAAAGATGTGGTAAGAGTT 617
	Query 178 GCCGTCTCCGATGGATTAATTACTTGAGACCGGACCTTAAACGCGGTAATTTTACTGAAG 237
	| | | ||||||| ||||| | ||||| || || ||| | || |||||||||||||
	Sbjct 616 GTAGATTGAGATGGATGAATTATCTAAGACCAGATCTCAAAAGAGGCAATTTTACTGAAG 557
	Query 238 AAGAAGATGAACTCATTATCAAACTCCATAGCCTCCTTGGTAACAAATGGTCACTTATAG 297
	|||||||||||||||| ||||| ||||||||| | || |||||||||||||| | ||||
	Sbjct 556 AAGAAGATGAACTCATCATCAAGCTCCATAGCTTGCTCGGTAACAAATGGTCTTTAATAG 497
	Query 298 CCGGAAGATTACCAGGAAGAACAGATAATGAGATAAAAAATTACTGGAATACGCACAT-A 356
	| || ||||||||||||||||||||||| ||||| || || || ||||| || || || |
	Sbjct 496 CTGGGAGATTACCAGGAAGAACAGATAACGAGATCAAGAACTATTGGAACACTCATATCA 437
	Query 357 AGAAGGAAGCTTTTGAGTCGGGGCATTGATCCAA 390
	|| ||||||||| | || || || ||||||||||
	Sbjct 436 AG-AGGAAGCTTCTCAGCCGTGGGATTGATCCAA 404
	Lambda K H
	1.33 0.621 1.12
	Gapped
	Lambda K H
	1.28 0.460 0.850
	Effective search space used: 326667943382
	Query= Contig2
	Length=1009
	***** No hits found *****
	Lambda K H
	1.33 0.621 1.12
	Gapped
	Lambda K H
	1.28 0.460 0.850
	Effective search space used: 350998085934
	Query= Contig3
	Length=529
	***** No hits found *****
	Lambda K H
	1.33 0.621 1.12
	Gapped
	Lambda K H
	1.28 0.460 0.850
	Effective search space used: 180381608828
	Query= Contig4
	Length=896
	Score E
	Sequences producing significant alignments: (Bits) Value
	gi|152034016|gb|AU239642.2|AU239642 EST AU239642 RAFL21 Arabido... 167 1e-039
	> gi|152034016|gb|AU239642.2|AU239642 EST AU239642 RAFL21 Arabidopsis
	thaliana cDNA clone RAFL21-11-C04 5', mRNA sequence.
	Length=632
	Score = 167 bits (90), Expect = 1e-039
	Identities = 260/345 (75%), Gaps = 2/345 (1%)
	Strand=Plus/Plus
	Query 232 ATTGCCAATACTAAGTCTTGGTTCCAATTCTATGGCGACGGCTTTTCTATTCGTGTTCCA 291
	||||| || ||||||||||||||||| | || ||| || || ||||| | |||||
	Sbjct 286 ATTGCGAACACTAAGTCTTGGTTCCAGTACTTTGGTAGTGGGTTCGCTATTAGGGTTCCT 345
	Query 292 CCGGAATTTCAGGACCTCACTGAGCCGGAGGATTATAATGCTGGCCTATCACTATATGGA 351
	|| || ||| | ||| ||| |||||| |||||||| ||| || | || || |||||
	Sbjct 346 CCTGACTTTGAAGACGTCAATGAGCCTGAGGATTACTCTGCGGGATTGTCTCTCTATGGT 405
	Query 352 GATAAGGCTAAGCCCAAAAAATTT-GCAGCACGTTTTGCTTCTTCTGATGGATCCGAAGT 410
	|| ||||| ||||| | ||| ||| || || || || || |||||||||| |||||
	Sbjct 406 GACAAGGCAAAGCC-ACAAACTTTCGCCGCCCGGTTCCAAACTCCTGATGGATCAGAAGT 464
	Query 411 TTTAAGTGTCATAATTCGTCCATCCAATCAGCTGAAGATCACTTTCTTAGAGGCTAAAGA 470
	||| ||||| | |||||||| || ||||| || ||||||||||||||||||||||||||
	Sbjct 465 TTTGAGTGTAGTCATTCGTCCTTCAAATCAACTTAAGATCACTTTCTTAGAGGCTAAAGA 524
	Query 471 TATTACTGATTTAGGTTCACTTAAGGAGGCAGCAAAAATATTTGTTCCAGCTGGCTCAAC 530
	||| ||||||| || ||| | |||| || |||| | | |||||||||| || ||||
	Sbjct 525 TATATCTGATTTGGGATCATTGAAGGCAGCTGCAAGACTTTTTGTTCCAGGTGCNGCAAC 584
	Query 531 ACTATATTCTGTCCGCACAATAAAAATTAAAGAAGATGAGGGTTT 575
	| | || |||| || ||||| || | || ||||| || |||||
	Sbjct 585 AATTTACTCTGCTCGTACAATCAAGGTAAAGGAAGAAGAAGGTTT 629
	Lambda K H
	1.33 0.621 1.12
	Gapped
	Lambda K H
	1.28 0.460 0.850
	Effective search space used: 310567113752

view raw biostars-148979.txt hosted with ❤ by GitHub

CONTIG FILE

>Contig1
GAGCTAAATAATTTGAATCAATGGGAAGATCACCGTGTTGTGAAAAAGCACATACAAATA
AAGGAGCTTGGACTAAAGAAGAAGATGAACGACTTATTTCTTATATTAAAACTCACGGCG
AAGGTTGCTGGAGATCCCTTCCTAAAGCTGCCGGACTTCTCCGATGCGGTAAAAGTTGCC
GTCTCCGATGGATTAATTACTTGAGACCGGACCTTAAACGCGGTAATTTTACTGAAGAAG
AAGATGAACTCATTATCAAACTCCATAGCCTCCTTGGTAACAAATGGTCACTTATAGCCG
GAAGATTACCAGGAAGAACAGATAATGAGATAAAAAATTACTGGAATACGCACATAAGAA
GGAAGCTTTTGAGTCGGGGCATTGATCCAACGACACACAGGCCTGTTAACGAGCCTGGTA
CAACGCAAAAAGTCACAACAATTTCATTTGCAGGTGGAGATCATAAAACTAAAGATATTG
AAGAAGATCATAATAAGATGATAAATGTCAAAGCTGAATCTGGGTTGAGTCAATTAGAAG
ATGAAATTATTAGTAGCAGTCCATTTCGAGAACAGTGTCCTGATTTAAATCTTGAGCTCA
GAATTAGCCCTCCTTCTCTACAAAATTACCAACATAGCCCCTCAAGGTGTTTTGCATGCA
GTTTGGGTATACAAAATAGTAAAGATTGCAATTGCAGTAAAAATAATATTGCAAGTTATA
ACTTTTTAGGATTAAAGAGTAATGGTGTTTTGGACTATAGAACTTTAGAAACTAAGTGAA
TTTTTATTATAAATCTTTTTTTCCCTCGTGTATTTGGGTTAAAAAAACAAGAAGAGAGAA
TCGAGAAAGATATTCCTATTAGTTTAAGTTCTTTCGAATTTTCTCTTATTTGTAAAATTT
CAAGTATTACTATATACGATATATTATATTAAGTTGAAAAG
>Contig2
GCTCTTCCAACAACAACAACAATGCCTCATCAAAAGCCTCTTTCTCTCATTCTTCTATCT
ACACTCCCACTTCTTTTCATTCTCACACAAGCTCAATCACCAACAGCACCAGCACCAGCA
CCCTCAGGACCAATAGACATCTTTGCAATCCTCAAAAAAGAAGGACAATACAACACATTC
ATCAAGTTCCTAAATGAATCACAAGTTGGTAACCAAATCAACAACCAAGTAAACAACTCC
AACCAAGGCATGACAGTTTTGGCACCATCAGACAATGCATTTAACAACCTCCCAAGTGGT
ACACTCAACCAACTAAATGACCAACAAAAAGTACAACTCATTTTGAACCATGTCATACCA
AAGTTCTACACATTTGATGACTTACAAACAGTAAGCAACCCTGTTAGAACACAAGCAACA
GGGCCTAAAGGTGAGCCTTTTGGACTTAACTTTACTGGAAGTAACAATCAAGTGAATGTC
TCATCTGGTTCTGTTGTTACAAACATTTATAATGCTATTAGAAAAGACCCCCCATTGGCT
GTTTTTCAATTAGACAAAGTTTTAGTACCTTCTCAGTTTACTGATCCATCTAGTGATGAT
GATGCCCCTGCACCTACTAAACCCAAGAATGGTACTAGTAATGATAAAACAACAGCTGAT
GAGCCATCACCAGCAAGTAACACTAAGCCAAATGATGCTAAAAGGATCAGTGGTGGGATT
CTTGGATTGGTTTGTGGTGTTTTCTTGATGGCAACACTATCTTGAAGGGGGCTACAGAGT
TGTTAACTTTATGATCTTTTGCTTATACTAAGCCATTTTGTATTACATTGTTTTCTTCAA
GATTGATTGTTTTTGTTCAAAAAAGAAGGGGGGGGGGGAAAAAAAAACCCCCCTGCGGAA
AAGAGCGGGGAAAGCACCAAAAAGCCACCGACCAAAAGCACCAACTCACAAAAGGTGCGC
AGACGCGGAAAGGGGAAAAGGAAAAAATGTGAAAGCTTGTTATAGTTTG
>Contig3
AAACTGTAATTAGACTTCTCTGCTAAGTTTCTGCTGTATTTGGATTCTCCGGCGAACATT
AATATCTAACCATGACCGGCGGTGGAGGCGATGCCGCATCGCCGCCTCTATCCTCACAGT
CAACTCCATCCAACGGTGGGGAATTCCTTCTTCAATTGCTTCAGAATCATCCGCATCAAC
TTCACTCTCAGCCTCAACCGCCACTGCGGCCGGAGTTGCAGAATCTGCCGCATGATCCAG
CAGTTGCAGCAGTAGGTCCTAGTATGCCCTACCCGCCATTGTTCCATACTCCTACAAACC
CTTCTGTTTTGCCCTATTCTCACTCTCCTCCTCTGTTTGTACCTCATAACTTCTTCATTC
GAGGGTTTCTCCAAAACCCTAATTCTGGCCATACCACTAACCCCAATTACTCATCTCCGC
CTGCCCCAAGTGGGTTCAGTCAATATCACCATGCGAGTCCACTTGGATTTGGATCAGTCG
GAGAAAACATGGGCAATTTGGGGATTTTCGGTGCCAATGCTAAGGCGAG
>Contig4
CATGTAATAGCATAGCATCCCCAATTTCACCCTCTCATGGCCATGTCCACGCTCCTCTCC
CTGTCCGTGTCTATCCACCCACCAAAACCTTTGCAAAAACCCAATTCAATGTGTACCCAA
CCTAACTCTATTTCGAGAAGACAAGTGTTTTTCACTGGTTCTAATTTATTGCTCTCTCAA
TTAATTCCAAAATCCGACGCCCAAACCAATTCCAATAGTTTTCTTTCAGGTATTGCCAAT
ACTAAGTCTTGGTTCCAATTCTATGGCGACGGCTTTTCTATTCGTGTTCCACCGGAATTT
CAGGACCTCACTGAGCCGGAGGATTATAATGCTGGCCTATCACTATATGGAGATAAGGCT
AAGCCCAAAAAATTTGCAGCACGTTTTGCTTCTTCTGATGGATCCGAAGTTTTAAGTGTC
ATAATTCGTCCATCCAATCAGCTGAAGATCACTTTCTTAGAGGCTAAAGATATTACTGAT
TTAGGTTCACTTAAGGAGGCAGCAAAAATATTTGTTCCAGCTGGCTCAACACTATATTCT
GTCCGCACAATAAAAATTAAAGAAGATGAGGGTTTCAGGACATACTATTTTTATGAATTT
GTGAGAAATGAGCAACACGTTGCATTAGTGGCTGGTGTTAACAGTGGAAAGGCCGTCATT
GCTGGTGCCACGGCCCCCGAAAGCAAATGGGCCGAGGATGGTTTGAAGCTCCGATCTGCT
GCAGTATCAATGACAATTCTATAAGCAGAATGTGAGTATATATATAGGTTCTATTTCAAT
GATGATGAATTTATATACAAATATTGAGGATCAAAGTTTTCTTATTATCATCTAATCTCA
GCCAAGGATTAACAATCTCCATCATCCATTCAATAGCAATGTTTCTGCTGTTTTGC

[iraun]

If the blast output is in tabular format, you can extract headers from your contig fasta file to headers.txt file, and simply use a grep -v -F -f headers.txt blast.tab to extract all contigs that are not present in blast file. But, as roy.granit has pointed out, it could be helpful to provide an example of input and desired output files. If I understand well the problem, its not necessary to write a perl script, but of course it can be solved also with perl.

[vinij80]

Above mentioned are the blast result file and the contig file

[vinij80]

contig2 and contig 3 show no blast hits so I need to extract these 2 contig sequences into a separate text file

Answer 1

[iraun]

1) Extract names of contigs without hit in blast:

grep -B5 "***** No hits found" blast.txt | grep Query | sed 's/Query= //g' > ids

2) Extract fasta records of those contigs without hit:

cat ids | xargs -n 1 samtools faidx contigs.fa > contigs_nohit.fa

[vinij80]

I am a beginner in perl. I did not understand what grep is, can you explain me how to run this script???

Can you write perl script for this??

[iraun]

This is not perl, is bash. You can open a linux terminal, write these two lines, and you will have desired output in contig_nohit.fa file. I would recommend you to read a little bit about basic bash commands: http://ss64.com/bash/.

[vinij80]

The first command is working..But by run the second command it shows that

[_razf_open] fail to open contigs.fa
[fai_build] fail to open the fasta file contigs.fa
[fai_load] fail to open FASTA index

Please give me the solution for this problem...

[iraun]

What's the name of your file containing the contigs? I named it 'contigs.fa' as an example, but you should replace this name with your file name.

[vinij80]

I tried like that..but it shows that

[fai_load] build FASTA index
not found in FASTA file returning empty sequence
xargs: samtools: terminated by signal 11

[vinij80]

Thankyou Airan for your help...