How to customize the output of my BLASTP output tabular form
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Entering edit mode
2.5 years ago
Yuri • 0

I'm trying to align the output of I got previously to against the swissprot database, and I need to have an output in tabular form with -qseqid -sacc -qlen -slen -length -nident -pident -evalue -stitle and I want to set the evalue less than 1e-10. Here is my code :

#!/usr/bin/env bash
blastp -query Trinity.fasta.transdecoder.pep \
    -db swissprot \
    -outfmt "6 qseqid sacc qlen slen length nident pident evalue stitle" -evalue 1e-10 1>Predict.txt \
    2>wrongPredicted.err

However this is the first several lines of output I got in the txt file:

TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   Q964E0  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   Q964D9  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   P53472  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoskeletal 1A; AltName: Full=Actin, cytoskeletal IA; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   P92179  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   Q964E1  400     376     376     363     96.54   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   Q964E2  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   P69004  400     376     376     364     96.81   0.0     RecName: Full=Actin-15B; Flags: Precursor

The problem is that all the evalue is 0.0 for some reasons, because what I want is something like this:

TRINITY_DN8_c0_g1_i1 Q5ZKK7 283 788 64 53 82.81 1e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3
TRINITY_DN8_c0_g1_i1 Q7ZVV1 283 782 64 53 82.81 3e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3
TRINITY_DN8_c0_g1_i1 Q1RMT1 283 782 64 52 81.25 6e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3
TRINITY_DN8_c0_g1_i1 Q5RA62 283 782 64 52 81.25 7e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3
TRINITY_DN8_c0_g1_i1 Q60HG1 283 782 64 52 81.25 7e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3

The 8th column should be valid evalue. Need some help! Thank you!

Linux Bash BLAST • 558 views
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Entering edit mode

My guess is that output should say 0E0 instead of 0.0 considering pident is over 96%. see: Blast e-value 0E0

Examine the alignment to be sure by doing a quick blast search.

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