python newbie - only else statement is printed

Question

[mdrnao]

Complete beginner so I'm sorry if this is obvious!

I have a file which is name | +/- or IG_name | 0 in a long list.

S1      +
IG_S1   0
S2      -
IG_S3   0
S3      +
S4      -
dnaA    +
IG_dnaA 0

Everything which starts with IG_ has a corresponding name. I want to add the + or - to the IG_name.

The information is gene names and strand information, IG = intergenic region. Basically I want to know which strand the intergenic region is on.

what I want:

open file
if starts with IG_*
    find the line with *
    print("IG_" and the line it found)
else 
    print(line)

what I have:

with open(sys.argv[2]) as geneInfo:
    with open(sys.argv[1]) as origin:

            for line in origin:
                    if line.startswith("IG_"):
                            name = line.split("_")[1]
                            nname = name[:-3]
                            for newline in geneInfo:
                                    if re.match(nname, newline):
                                            print("IG_"+newline)
                    else:
                            print(line)

where origin is the mixed list and geneInfo has only the names not IG_names.

With this code I end up with a list containing only the else statements.

S1  +

S2  -

S3  +

S4  -

dnaA    +

My problem is that I don't know what is wrong to search!

[Zaag]

What 2 files do you start with?

[mdrnao]

"where origin is the mixed list and geneInfo has only the names not IG_names"

So origin is the first example, and geneInfo has everything except the ones which start with IG.

[Istvan Albert]

What others are saying is that you should show just a few lines of each input file, then show the exact command as you invoke it. These to ingredients are necessary to troubleshoot.

[mdrnao]

Sorry, I should have made my other file more obvious! second file looks like this:

S1  +
S2  -
S3  +
S4  -
dnaA    +

Answer 1

[Zaag]

you need to open the file twice and there is a double loop, so there should be a few better ways to do this.

NIG = []
with open('input.txt') as f:
      for line in f:
              line = line.strip()
              if not line.startswith('IG_'):
                      name, strand = line.split()
                      NIG.append([name, strand])

with open('ig_inout.txt') as f:
      for line in f:
              line = line.strip()

              if line.startswith('IG_'):
                      [print(line,  i[1]) for i in NIG if i[0] == line.split()[0].split('_')[1] ]
              else:
                      print(line)

but this gives me this output:

S1      +
IG_S1   0 +
S2      -
IG_S3   0 +
S3      +
S4      -
dnaA    +
IG_dnaA 0 +

[mdrnao]

Excellent! Thank you!

Would you mind explaining the second loop?

[print(line,  i[1]) for i in NIG if i[0] == line.split()[0].split('_')[1] ]

this is confusing me!

[Zaag]

You can write it like this:

for i in NIG:
    if i[0] == line.split()[0].split('_')[1]:
        print(line,  i[1])

For each entry without IG:

    if NAME is the same as the second part of IG_NAME

        print the line of the file and the + or the -
  

[WouterDeCoster]

Hi Zaag, why not use a dictionary? I reused most of your code: (untested!)

stranddict = {}
with open('input.txt') as f:
      for line in f:
              if not line.startswith('IG_'):
                      name, strand = line.strip().split('\t')
                      NIG[name] = strand

with open('ig_inout.txt') as f:
      for line in f:
              if line.startswith('IG_'):
                      print(line.split('\t')[0] + "\t" + stranddict[line.split('\t')[0].replace("IG_", "")]
              else:
                      print(line)