how linearize nucleotide lines in axt file

Question

[resug]

Hi,

I am trying to make the nucleotide lines linear, instead of split every 60 nucleotides, and keeping the blank lines between every entry. So the axt file should look from this:

Lm_g1002.t1-Lp_g998.t1
ATGAGGTGCTTAAAGATTTTTCAGTTCATAACATCTTTGACTAAATCCTCTGGCTCAACT
ATAGCTGCTCGGCTAACTGTCTTAGCCCAGCAGTGTTCAACTTGTCATGACTTAGCTTAT
CTTGGTTCAGCTGGTCTTGGTTTAGCTGATATTGGTTCAAATGTT
ATGAGGTGCTTAAAGATTTTTCAGTTCATAACATCTTTGACTAAATCCTCTGGCTCAACT
ATAGCTGCTCGGCTAACTGTCTTAGCCCAGCAGTGTTCAACTTGTCATGACTTAGCTTAT
CTTGGTTCAGCTGGTCTTGGTTTAGCTGATATTGGTTCAAATGTT

Lm_g1010.t1-Lp_g1011.t2
ATGTCGAAGGAATTCAACGTCCCTCCAGTAGTTTTCCCCTCTGGCGGAAACCCAGGCCCA
AACCCTAACCTCCACGACGACGCCGATCTTTCCGGCCCCGTCCTCTGCCTCATGATGTTC
GGCCTCTTCCAGCTCCTCGCCGGAAAGATCCACTTCGGTATCATCCTCGGTTGGGTAACC
GTTTCTGCGCTTTTTCTCTACGTTGTTTTCAATATGCTTGCTGGTCGTAACGGGCGGTGT
TGTCATTTCCGG------CGTCGCCGCGGTTTTTGTGATTTG------------------
------------------------------------------------------------
---GTC
ATGTCGAAGGAATTCAACGTCCCTCCAGTAGTTTTCCCCTCTGGCGGAAACCCAGGCCCA
AACCCTAACCTCCACGACGACGCCGATCTTTCCGGCCCCGTCCTCTGCCTCATGATGTTC
GGCCTCTTCCAGCTCCTCGCCGGAAAGATCCACTTCGGTATCATCCTCGGTTGGGTAACC
GTTTCTGCGCTTTTTCTCTACGTTGTTTTCAATATGCTTGCTGGTCGTAACGGTAATTTG
GATCTTTACCGGTGTGTTAGTTTGATCGGGTATTGTATGCTACCTATGGTGATTTTGTCC
CATCGTGGATTAGTTGCGTATGGTTGCTTTCTTATTTACACTTTGTTTTCGCTTCTTGTC
GTGTTT

Lm_g1018.t1-Lp_g1004.t1
ATGGCTTTGAATAGCAGTGTCAGATCTACTGCCAAGTTAATCGCTTCTTCTCATTCATCC
CATCAGGGATTGAAAATGTCCCTCGCGGTGTTCAGTGCTTTCAGCATTGGTGTTGCAGTT
CCTATCTATGCTGTCATTTTCCAGCAAAAGAAGACAGCTTCTGGT
ATGGCTTTGAATAGCAGTGTCAGATCTACTGCCAAGTTAATCGCTTCTTCTCATTCATCC
CATCAGGGATTGAAAATGTCCCTCGCGGTGTTCACTGCTTTCAGCATTGGTGTTGCAGTT
CCTATCTATGCTGTCATTTTCCAGCAAAAGAAGACAGCTTCTGTT

Lm_g100.t1-Lp_g97.t1
------ATGGATTTTCACACTCTTTCCAGAAAACAGCTCCAGAGTCTCTGCAAGAAGAAC
GATATTGAGAAAATGGATGACTTCTCTGATGTTACTGGCACAGCGTTAGCTTCTCTTGAG
GTTTCCACTGAATCTTCTGCAGACAAATGCAGCATGGATGCAGAAAATGACTTT------
------------------------------------------------------------
------------------------CTTGAGTCTTCACTGGTGGATGTAGTTGTACATGAA
AGCAAGACTACAAATGTTGTAAAGGAAGTGGAGAAGAAAAGAACTGCACTGCAGACACTG
CCAGAGAACATGATGGAGAAA
ATGACCATGGATTTTCACACTCTTTCCAGAAAACAGCTCCAGAGTCTCTGCAAGAAGAAC
GATATTGAGAAAATGGATGACTTCTCTGATGTTACTGGCACAGCGTTAGCTTCTCTTGAG
GTTTCCACTGAATCTTCTGCAGACAAATGCAGCATGGATGCAGAAAATGACTTTCTTGAG
ACATCTTTTGAGAAGGCAATGACAATTATGGACCTCTGTTCTGAATCCTTAGCAGCAGAC
AAAATGAATGCTGAAAATGCCACTCTCGAGTCTTCATTGGTCGATGTAGTTGTACATGAA
AGCAAGACTACAAATGTTGTAAAGGAAGTGGAGAAGAAAAGAACTGCACTGCAGACACTG
CCAGAGAACATGATGGAGAAA

To this:

Lm_g1002.t1-Lp_g998.t1
ATGAGGTGCTTAAAGATTTTTCAGTTCATAACATCTTTGACTAAATCCTCTGGCTCAACTATAGCTGCTCGGCTAACTGTCTTAGCCCAGCAGTGTTCAACTTGTCATGACTTAGCTTATCTTGGTTCAGCTGGTCTTGGTTTAGCTGATATTGGTTCAAATGTT
ATGAGGTGCTTAAAGATTTTTCAGTTCATAACATCTTTGACTAAATCCTCTGGCTCAACTATAGCTGCTCGGCTAACTGTCTTAGCCCAGCAGTGTTCAACTTGTCATGACTTAGCTTATCTTGGTTCAGCTGGTCTTGGTTTAGCTGATATTGGTTCAAATGTT

Lm_g1010.t1-Lp_g1011.t2
ATGTCGAAGGAATTCAACGTCCCTCCAGTAGTTTTCCCCTCTGGCGGAAACCCAGGCCCAAACCCTAACCTCCACGACGACGCCGATCTTTCCGGCCCCGTCCTCTGCCTCATGATGTTCGGCCTCTTCCAGCTCCTCGCCGGAAAGATCCACTTCGGTATCATCCTCGGTTGGGTAACCGTTTCTGCGCTTTTTCTCTACGTTGTTTTCAATATGCTTGCTGGTCGTAACGGGCGGTGTTGTCATTTCCGG------CGTCGCCGCGGTTTTTGTGATTTG---------------------------------------------------------------------------------GTC
ATGTCGAAGGAATTCAACGTCCCTCCAGTAGTTTTCCCCTCTGGCGGAAACCCAGGCCCAAACCCTAACCTCCACGACGACGCCGATCTTTCCGGCCCCGTCCTCTGCCTCATGATGTTCGGCCTCTTCCAGCTCCTCGCCGGAAAGATCCACTTCGGTATCATCCTCGGTTGGGTAACCGTTTCTGCGCTTTTTCTCTACGTTGTTTTCAATATGCTTGCTGGTCGTAACGGTAATTTGGATCTTTACCGGTGTGTTAGTTTGATCGGGTATTGTATGCTACCTATGGTGATTTTGTCCCATCGTGGATTAGTTGCGTATGGTTGCTTTCTTATTTACACTTTGTTTTCGCTTCTTGTCGTGTTT

Lm_g1018.t1-Lp_g1004.t1
ATGGCTTTGAATAGCAGTGTCAGATCTACTGCCAAGTTAATCGCTTCTTCTCATTCATCCCATCAGGGATTGAAAATGTCCCTCGCGGTGTTCAGTGCTTTCAGCATTGGTGTTGCAGTTCCTATCTATGCTGTCATTTTCCAGCAAAAGAAGACAGCTTCTGGT
ATGGCTTTGAATAGCAGTGTCAGATCTACTGCCAAGTTAATCGCTTCTTCTCATTCATCCCATCAGGGATTGAAAATGTCCCTCGCGGTGTTCACTGCTTTCAGCATTGGTGTTGCAGTTCCTATCTATGCTGTCATTTTCCAGCAAAAGAAGACAGCTTCTGTT

Lm_g100.t1-Lp_g97.t1
------ATGGATTTTCACACTCTTTCCAGAAAACAGCTCCAGAGTCTCTGCAAGAAGAACGATATTGAGAAAATGGATGACTTCTCTGATGTTACTGGCACAGCGTTAGCTTCTCTTGAGGTTTCCACTGAATCTTCTGCAGACAAATGCAGCATGGATGCAGAAAATGACTTT------------------------------------------------------------------------------------------CTTGAGTCTTCACTGGTGGATGTAGTTGTACATGAAAGCAAGACTACAAATGTTGTAAAGGAAGTGGAGAAGAAAAGAACTGCACTGCAGACACTGCCAGAGAACATGATGGAGAAA
ATGACCATGGATTTTCACACTCTTTCCAGAAAACAGCTCCAGAGTCTCTGCAAGAAGAACGATATTGAGAAAATGGATGACTTCTCTGATGTTACTGGCACAGCGTTAGCTTCTCTTGAGGTTTCCACTGAATCTTCTGCAGACAAATGCAGCATGGATGCAGAAAATGACTTTCTTGAGACATCTTTTGAGAAGGCAATGACAATTATGGACCTCTGTTCTGAATCCTTAGCAGCAGACAAAATGAATGCTGAAAATGCCACTCTCGAGTCTTCATTGGTCGATGTAGTTGTACATGAAAGCAAGACTACAAATGTTGTAAAGGAAGTGGAGAAGAAAAGAACTGCACTGCAGACACTGCCAGAGAACATGATGGAGAAA

I would appreciate your help. Thank you.

Rom

[GenoMax]

Using Pierre Lindenbaum 's linearize fasta code

awk '/^Lm/ {printf("%s%s\t",(N>0?"\n\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' < original.fa | tr "\t" "\n" > reformat.fa

[resug]

There are two sequences per entry, and the provided awk script has merged the two sequences into a single linear sequence. But the objective is to make two linear sequences. Could this be possible please? Thank you!

The above provided script produces one linear sequence:

Lm_g1002.t1-Lp_g998.t1
ATGAGGTGCTTAAAGATTTTTCAGTTCATAACATCTTTGACTAAATCCTCTGGCTCAACTATAGCTGCTCGGCTAACTGTCTTAGCCCAGCAGTGTTCAACTTGTCATGACTTAGCTTATCTTGGTTCAGCTGGTCTTGGTTTAGCTGATATTGGTTCAAATGTTATGAGGTGCTTAAAGATTTTTCAGTTCATAACATCTTTGACTAAATCCTCTGGCTCAACTATAGCTGCTCGGCTAACTGTCTTAGCCCAGCAGTGTTCAACTTGTCATGACTTAGCTTATCTTGGTTCAGCTGGTCTTGGTTTAGCTGATATTGGTTCAAATGTT

The goal is to make two linear sequences:

Lm_g1002.t1-Lp_g998.t1
ATGAGGTGCTTAAAGATTTTTCAGTTCATAACATCTTTGACTAAATCCTCTGGCTCAACTATAGCTGCTCGGCTAACTGTCTTAGCCCAGCAGTGTTCAACTTGTCATGACTTAGCTTATCTTGGTTCAGCTGGTCTTGGTTTAGCTGATATTGGTTCAAATGTT
ATGAGGTGCTTAAAGATTTTTCAGTTCATAACATCTTTGACTAAATCCTCTGGCTCAACTATAGCTGCTCGGCTAACTGTCTTAGCCCAGCAGTGTTCAACTTGTCATGACTTAGCTTATCTTGGTTCAGCTGGTCTTGGTTTAGCTGATATTGGTTCAAATGTT

[rfran010]

I think that's a tough one. Will the two sequences under each header always be equal lengths? If so, I'm thinking a custom script that can split those lines based on halving the amount of lines under each header.

Here's my attempt (disclaimer, I am a python novice):

#!/usr/bin/python3

import sys

# open the input for reading and an output for writing and initialize a list
input = open(sys.argv[1],'r')
output = open(sys.argv[2],'w')
lines = []

# begin iterating through the input.
# if the line is the first line, then record as the header, with leading/trailing whitespace removed.
# iterate through subsequent lines appending them to a list.
# when encountering an empty line (signaling the end of a section), split the list into equal parts and concatenate the list into two separate lines.
# re-initialize the list and restart the iterator to begin a new section, recording the next line as a header and so on.
# after the last line was read, determine if file ended with an empty line.
# If input file ends with empty line, do nothing since last section is already output (including the empty line).
# If input file ends immediately after the string, then output the last section without an empty line.

i = 1

for line in iter(input):
  if i == 1:
    header=line.strip()
    i += 1
  elif line in ['\n', '\r\n']:
    num = int(((i/2) - 2))
    i = 1
    output.write(header+"\n"+"".join(lines[0:num])+"\n"+"".join(lines[num + 1:-1])+'\n'+'\n')
    lines = []
  else:
    lines.append(line.rstrip())
    i += 1

if lines != []:
  num = int(((i/2) - 2))
  output.write(header+"\n"+"".join(lines[0:num])+"\n"+"".join(lines[num + 1:-1])+'\n')

This is designed to be placed in a script e.g. "linearize.py" and run with an input file and desired output filename as arguments (script included as google drive link below)

python3 linearize.py inputFile.txt outputFileName.txt

linearize.py

[dariober]

(+1) I edited usr/bin/python3 to /usr/bin/python3. Why not posting it as an answer?