Filter assembly contigs bei depth/coverage

Question

[thorbensieksmeyer]

Hi all,

is there an easy way to filter a contig fasta file which looks like this by the depth stated in the identifier e.g. make a new file with contigs with depth <2.0? Thanks in advance :)

>1 length=282707 depth=1.00x
TACGAAAAAAAAGCAAAAAAAAGAGGAGGAGGCTCACGCCTCCCCCTCTCCCTTTCAGCTTACGCCACCA
GCACGTCAGTCCGCGTCAACAGCATGCCCGTCAATCGGCGCCCTTATGTTGGGACATGATCAATGACAGG
ACACCCGGAACTTGTCTTTGTGCAGGCCTGTCCTCATACGTAAGGGGCTTTGCATCCCGCATCGCAATGA

>2 length=26815 depth=3.45x
CCAGGGAAGCAGCAGTCAACACGCTAAAAACCTGAAATCAGGCACAAGAGAAGTCAATCAAAGGTTTTTC
GAACCCTCCAGGTTTGACCCCGCAAAAGACCTCGCCAACCAAAAAAAGCACAAACTGTCTCTGGCCTTTG
GCGACCGTATTTTCGAGGACGATAATCACCTGATCTTGCCCACCATCCGCATTGAGGATGAGGAGGATCG

>3 length=24243 depth=1.02x
CACTTTTTTCGAAAAAACAATCTCCGCCTGAATTCGGATCGCGGTTAACTGCCGATTTCGACGGGCATCT
TTTTATCGTCCCCTTACCAGCAGCACCAGACGAAGTGGTATAATATAACAATAATCCGTTGGGCAGGATA
ACTGCTATTATCAAAATCAGCGCAGACCCTGCCAAAGACGGCCCGTAATATGCGGCCATCGGGGAGCGGC
CGCCGTAGCTGTTACGCCGTACTGCCCCAATCCATGTTCCATTCAAGGCAAGAGACGCACAAACCGATGC
AACCTGCTCCCAAGGCAACACTTCTCACGCGGCTCAATGAACAGATCGCCGTCAAGATGACCTTCATTTT
TGGAAGCATCTGGTGCGTTTACGCCTTCCTTGTCTTCTCCCTGATCCCGCTTGCCGCACCGGGATGGCAG

Answer 1

[Pierre Lindenbaum]

awk -F '[=x ]' '/^>/ {P=($5 < 2.0)}  {if(P) print}' in.fasta

[thorbensieksmeyer]

It worked great - thanks Pierre